The author hints in one of the later arcs, Musubimonogatari, that Araragi will most likely marry only one woman in his life, and that is Hitagi Senjougahara. But to answer your question, the obvious choice is Shinobu. Otherwise why would the author have Araragi say that line in Kizumonogatari over and over if it wasn't even that important? Over the course of their relationship, Araragi had 4 break-ups with Senjou with most reasons being quite petty... On the other hand, his relationship with Shinobu has always been consistent, unshakeable, and stable despite everyone moving on, including Hanekawa and Senjou who started working overseas.
At the very least, Musubimono's silence as regards Shinobu's and Araragi's relationship is still in keeping with Araragi's promise that he has no intention of letting Shinobu go even if he ends up seeing his loved ones/family die before he does.
As for Hanekawa, there are enough hints to suggest his feelings for her must have been far deeper than he's willing to let on. In fact Senjou continues to be jealous of Hanekawa who is unaware that she's partly the reason Senjou seems dissatisfied with her relationship with Araragi. Both Senjou's and Araragi's insecurities about living apart from each other seem to stem from some subconscious feeling that if they stay apart for too long, they might never reconcile at all.
This kind of insecurity may be relatable, but it's also far from being psychologically healthy...
More disturbing is that when Araragi is told that Hanekawa returned from overseas just to visit him, he says (again, in Musubimononogatari) that such likelihood is impossible. After all, he's become nothing but insignificant through the years, and yet, his becoming the man Hanekawa least cares about only makes him the happiest...
Ironically there are arrangements between Araragi and Hanekawa as to how she might let him know in case she dies. Araragi seems hell-bent on not letting her die and even says at one point that his love for Hanekawa goes beyond wanting to be with her forever.
So again whatever Araragi admits as to his feelings for Hanekawa sounds miserably dishonest. It is as if until the very end, pushing away Hanekawa is a life goal in itself, a heroic act of self-denial and sacrifice that he also attempts at Kizumonogatari, except that the pretense back then was too illogical to be convincing at any point.
One way of explaining it is to go back to those arcs relating to Shinobu's past. Shinobu says that in the past she's been cursed to have people sacrificing their most treasured possessions (even taking their own lives) as a love offering to her. It's possible that Araragi had made up his mind to be with Senjou as a way of keeping Hanekawa or his most prized possession at a safe distance. One proof is that when Oshino asks him if he's in love with Hanekawa, Araragi merely repeats the same denials. Yet while speaking his eyes become emotional, as if he's finally made up his mind to not love Hanekawa even if that decision hurts like hell.
But this only goes back to Shinobu being the ultimate love interest even if Araragi doesn't express it verbally all the time. It might be the workings of the curse on Shinobu, but Araragi had all the chances to break that curse or bond, but he just kept reviving it when it's broken. Apparently the author wants Araragi to keep his hold on Shinobu as his true lifetime partner who outlives all his other precious relationships, including both Hanekawa and Senjou.
Even getting a job as a police officer for the first-ever agency in Japan investigating oddities and apparitions only says how much his ties with Shinobu influenced his major life decisions, whereas both Hanekawa and Senjou decided to take entirely oddity-unrelated professions. Araragi is smart enough to pursue similar careers, but he didn't do this.
There are various other hints everywhere (both in the LN and the anime) but the strongest ones are convincing enough.
For example, in the end of the world chapter/episode where Araragi and Shinobu time travel, Araragi says how he was more shocked that he wasn't shocked at all that everybody, including Hanekawa and Senjou, must have disappeared or died, and that he and Shinobu were the only remaining survivors. As for Musubimonogatari, even if there are vague hints or foreshadowing of marriage between Hitagi and Araragi, we don't really see how Araragi intends to have a "normal" family life with Hitagi. I mean, it seems pretty obvious that his vampire blood may result in Hitagi giving birth to monsters or oddities if he impregnates her.
Although Araragi says he'd do anything to be with Senjou more, he merely falls back on that overly-repeated and bland "I love you" to comfort Senjou who seems to be in tears because of their previous break-up (the 4th).
To his benefit, Araragi's only 23 yrs. old so we can excuse his somewhat immature and reckless attitude toward his future with Senjou. In Shinobumonogatari, which happens a few years before Musubimonogatari (which is the latest arc chronologically speaking), we instead see an aspect of Shinobu's past, this time Araragi meeting Shinobu's original human soul in heaven and getting a direct kiss from her even if the original intention is different.
And believe me, the author comes up with ridiculous and obvious excuses like this everywhere.
So what is this all about? For me it's the author throwing hints that the bond between Araragi and Shinobu extends to the after-life that they can't help finding each other no matter what the circumstances are. Ironically, there are no signs that a deeper bond exists between him and any other character.
Next to Shinobu's and Araragi's intentional and accidental soul-mate moments, the I love you's with Senjou sound like hello.
Or basically you have Araragi being married to Senjou but continuing with his casual I love you but you're not the only special relationship I have sort of approach. He seems committed to the idea that he'll eventually die with Shinobu since he makes no move to break the vampire bond with Shinobu despite having plans to live together with Senjou as a married couple.
What kind of a guy is that, you might ask. Here's my answer.
Musubimonogatari gives closure to Senjou/Araragi fans (it seems all they ever ask is when the two are ever gonna get married). But the closure doesn't have to apply to Shinobu and Araragi. If only as a test of loyalty and true love, it's fairly obvious that all Araragi needed to do was to break his bond with Shinobu to be able to live a normal life alongside Senjou.
Instead, what Araragi does manage in Musubimonogatari is to regulate Shinobu's encounters with oddities, perhaps to minimize her getting injuries. We know that the more either of them gets injured, the more they needed to drink each other's blood to recover.
In the LN, Araragi describes his blood-drinking sessions with Shinobu as euphoria that makes him almost lose himself with pleasure. In other words, over-dependence is like sexual intoxication... hence there's enough reason for Oshino and the other oddity killers to caution Araragi lest his vampire instincts overtake him someday.
Sadly for Senjou fans, the author never lets Araragi give up his vampiric ties. Araragi doesn't even get bothered by the need to be a normal human to be able to have a normal future with Senjou, and Senjou, for her part, doesn't seem to ask much, as she probably knows Araragi will not sever this bond anyway.
And let's not forget that no one understands why he and Shinobu chose to remain bonded against all odds. But it does give us clues as to why Shinobu has never been seriously jealous with Senjou to begin with.
And most likely, Araragi also needs to be in a relationship with Senjou to keep the balance, as being with Hanekawa arouses his intense desire to be completely human, while being with Shinobu does the same for his vampire insticts.
Still, the best solution is to go back in time and fix things before Shinobu gets cut down by vampire slayers and meets Araragi. The problem is, the author doesn't want that route to untangle Araragi, Senjou, and Hanekawa... ^_^
He prefers the sado-masochist route that is a notch away from turning the story into absolute trash. In short, Senjou's and Araragi's foreshadowed marriage is nothing more than plot convenience that gets him to keep his harem even after marriage.
Hitagi and Araragi having kids possessed by apparitions or carrying "oddity" genes doesn't seem to be a bright future at all as Shinobu's Master even reveals that there are such things as vampire genes (see Shinobumonogatari). But Araragi doesn't even seem to be thinking of their relationship that far to bother with the scary consequences (tsk, tsk).
In any case, Musubi epilogue gives us the usual/typical Araragi saying in the usual, overly-casual way that he loves Senjou. Then she says the same thing she said back in Bakemono. But the mechanical, robotic echo effect of all this is troubling. Araragi's relationship it seems, has not really made any progress that might suggest that his love for Senjou has gone any deeper or made him more mature. He doesn't call her "beloved" or "my one and only" as a sign that their relationship has moved on from being just "lovers."
If you recall, it took him some time to call Senjou "Hitagi" though he had called Shinobu by her first name rather quickly and even used her nickname Kiss-shot just as easily. (When he realized that Shinobu's minion still called her by the same nickname he gets a bit jealous.)
To cut this short, nothing much changes.
Hence, we can say that for all intents and purposes, Araragi's desire to live and die with Shinobu has never changed either. Downplaying it for Senjou fans didn't mean that Araragi has chosen Senjou over her... in fact Shinobu can't be chosen over any other woman since Araragi has already decided a long time ago that whatever happens, he'll never let go of Shinobu even if it makes him feel guilty that he's the one who tied her to him forever.
In Kizu, we all know that heartbreaking line he keeps repeating in various arcs with regard to Shinobu:
"If you decide to end your life tomorrow, I'm fine ending my life by then. But if you decide to live for me for one more day, I'll try to live on for you as well... Perhaps ours is a story of scars, but it is a story I don't intend to recite to anyone..."
Therefore the curtain closes on Araragi not telling us his future with Shinobu but going so far as to suggest that even as he gets along with Senjou, his promise with Shinobu will go on with no one else needing to know how far they plan to take that master-servant/soulmate bond.
For me this is the only ending no one, not even Senjou, can overwrite. And it's the only ending that rescues this pseudo-philosophical, quasi love story from deteriorating into another teenage, harem-ecchi fantasy that desperately wants to be both entertaining and profound.